Run Plotter
genes = ['NTRK3', 'REEP5','RBP3','THRB','MEIS2','PRDM1','ONECUT1','TOX3','SIX6','OTX2','FGFR3','SEMA6D','TFAP2E']
for prefix in ['WT', 'G15','G16']:
print(prefix)
if prefix == 'WT':
file = '/Users/mcgaugheyd/data/chick_miruna/m006_scVelo.h5ad'
if prefix == 'G15':
file = '/Users/mcgaugheyd/data/chick_miruna/m007_scVelo.h5ad'
if prefix == 'G16':
file = '/Users/mcgaugheyd/data/chick_miruna/m008_scVelo.h5ad'
adata = sc.read_h5ad(file)
for g in genes:
scv.pl.velocity(adata, [g], show = False, save = prefix + '.' + g + '.png', dpi = 300, color ='seurat_clusters', palette=color_palette)
Each set goes: WT, G15, G16
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